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- PDB-1qqh: 2.1 A CRYSTAL STRUCTURE OF THE HUMAN PAPILLOMAVIRUS TYPE 18 E2 AC... -

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Basic information

Entry
Database: PDB / ID: 1qqh
Title2.1 A CRYSTAL STRUCTURE OF THE HUMAN PAPILLOMAVIRUS TYPE 18 E2 ACTIVATION DOMAIN
ComponentsPAPILLOMAVIRUS TRANSCRIPTION FACTOR E2
KeywordsVIRAL PROTEIN / AMPHIPATHIC HELIX / CASHEW/KIDNEY SHAPE
Function / homology
Function and homology information


host cytoskeleton / viral DNA genome replication / host cell mitochondrial membrane / regulation of DNA replication / DNA replication / DNA-binding transcription factor activity / nucleotide binding / DNA-templated transcription / host cell nucleus / DNA binding
Similarity search - Function
Regulatory Protein E2; Chain: A; Domain 2 / Papillomavirus E2 early protein domain / Papillomavirus E2, C-terminal / Papillomavirus E2, N-terminal / Regulatory protein E2 / E2 regulatory, transactivation domain / E2 regulatory, transactivation domain, subdomain 1 / E2 regulatory, transactivation domain, subdomain 2 / E2 (early) protein, N terminal / E2 (early) protein, C terminal ...Regulatory Protein E2; Chain: A; Domain 2 / Papillomavirus E2 early protein domain / Papillomavirus E2, C-terminal / Papillomavirus E2, N-terminal / Regulatory protein E2 / E2 regulatory, transactivation domain / E2 regulatory, transactivation domain, subdomain 1 / E2 regulatory, transactivation domain, subdomain 2 / E2 (early) protein, N terminal / E2 (early) protein, C terminal / E2/EBNA1, C-terminal / Beta Complex / Nucleotide-binding alpha-beta plait domain superfamily / Mainly Beta
Similarity search - Domain/homology
Regulatory protein E2
Similarity search - Component
Biological speciesHuman papillomavirus type 18
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsHarris, S.F. / Botchan, M.R.
CitationJournal: Science / Year: 1999
Title: Crystal structure of the human papillomavirus type 18 E2 activation domain.
Authors: Harris, S.F. / Botchan, M.R.
History
DepositionJun 5, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PAPILLOMAVIRUS TRANSCRIPTION FACTOR E2


Theoretical massNumber of molelcules
Total (without water)16,4811
Polymers16,4811
Non-polymers00
Water2,558142
1
A: PAPILLOMAVIRUS TRANSCRIPTION FACTOR E2

A: PAPILLOMAVIRUS TRANSCRIPTION FACTOR E2


Theoretical massNumber of molelcules
Total (without water)32,9622
Polymers32,9622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Unit cell
Length a, b, c (Å)76.240, 76.240, 158.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-355-

HOH

21A-364-

HOH

31A-400-

HOH

41A-428-

HOH

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Components

#1: Protein PAPILLOMAVIRUS TRANSCRIPTION FACTOR E2


Mass: 16481.137 Da / Num. of mol.: 1
Fragment: AMINO ACIDS 70-213 OF N-TERMINAL ACTIVATION DOMAIN
Mutation: R90A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 18 / Genus: Alphapapillomavirus / Species: Human papillomavirus - 18 / Plasmid: PGEX-2TK (GST FUSION) / Production host: Escherichia coli (E. coli) / Keywords: CONSISTENT WITH VARIANT GENBANK HPU89349 / References: UniProt: P06790
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 4.03 Å3/Da / Density % sol: 69.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 4
Details: AMMONIUM PHOSPHATE, TRIS, pH 4.0, VAPOR DIFFUSION, temperature 277.0K
Crystal grow
*PLUS
pH: 8.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18-12 mg/mlprotein1drop
2100 mM1dropNaCl
325 mMTris-HCl1drop
45 %glycerol1drop
510 mMdithiothreitol1drop
61.2-1.4 Mammonium phosphate1reservoir
7100 mMTris-HCl1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12001
21
31
41
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 20, 1997
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2MADMx-ray1
3MADMx-ray1
4MADMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 16635 / % possible obs: 99 % / Observed criterion σ(F): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 38.4 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 28.9
Reflection shellResolution: 2.1→2.17 Å / Rmerge(I) obs: 0.437
Reflection
*PLUS
Num. measured all: 135695

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.1→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2277455.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.297 1672 10.4 %
Rwork0.256 --
obs0.256 16126 97.2 %
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.68 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso mean: 49.8 Å2
Baniso -1Baniso -2Baniso -3
1-4.66 Å26.9 Å20 Å2
2--4.66 Å20 Å2
3----9.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1154 0 0 142 1296
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.612
X-RAY DIFFRACTIONc_scbond_it1.732
X-RAY DIFFRACTIONc_scangle_it2.82.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.359 259 10.5 %
Rwork0.333 2213 -
obs--91.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP

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